Incidental Mutation 'R1712:Ptcd3'
ID 190665
Institutional Source Beutler Lab
Gene Symbol Ptcd3
Ensembl Gene ENSMUSG00000063884
Gene Name pentatricopeptide repeat domain 3
Synonyms 2610034F17Rik, 2810422B04Rik
MMRRC Submission 039745-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1712 (G1)
Quality Score 181
Status Not validated
Chromosome 6
Chromosomal Location 71857622-71885734 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to A at 71885637 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Stop codon at position 30 (E30*)
Ref Sequence ENSEMBL: ENSMUSP00000146260 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055296] [ENSMUST00000082094] [ENSMUST00000206556] [ENSMUST00000206879]
AlphaFold Q14C51
Predicted Effect probably benign
Transcript: ENSMUST00000055296
SMART Domains Protein: ENSMUSP00000060858
Gene: ENSMUSG00000049553

DomainStartEndE-ValueType
RPOLA_N 302 649 8.97e-137 SMART
Pfam:RNA_pol_Rpb1_4 846 958 1.3e-26 PFAM
Pfam:RNA_pol_Rpb1_5 965 1669 7e-103 PFAM
low complexity region 1698 1708 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000082094
AA Change: E30*
SMART Domains Protein: ENSMUSP00000080743
Gene: ENSMUSG00000063884
AA Change: E30*

DomainStartEndE-ValueType
low complexity region 2 8 N/A INTRINSIC
low complexity region 216 227 N/A INTRINSIC
Pfam:PPR_2 253 300 1.4e-10 PFAM
Pfam:PPR_3 331 366 2.1e-4 PFAM
low complexity region 671 684 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205761
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205842
Predicted Effect probably null
Transcript: ENSMUST00000206284
AA Change: E22*
Predicted Effect probably benign
Transcript: ENSMUST00000206556
Predicted Effect probably null
Transcript: ENSMUST00000206879
AA Change: E30*
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206753
Meta Mutation Damage Score 0.9598 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.2%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Accs T A 2: 93,678,448 (GRCm39) E12D probably damaging Het
Ahnak2 C A 12: 112,748,998 (GRCm39) R283L probably benign Het
BC005624 T C 2: 30,864,020 (GRCm39) E191G probably damaging Het
C1galt1 A G 6: 7,871,217 (GRCm39) N351S probably benign Het
Ccdc162 T C 10: 41,415,427 (GRCm39) R2179G probably benign Het
Ccdc88c G A 12: 100,905,284 (GRCm39) T1108M probably benign Het
Cd47 T C 16: 49,714,543 (GRCm39) L184P probably damaging Het
Cdc40 T C 10: 40,717,372 (GRCm39) K440E probably damaging Het
Cenpe G A 3: 134,971,694 (GRCm39) V2262I probably damaging Het
Cep290 A G 10: 100,390,361 (GRCm39) K2035E probably benign Het
Cks1brt G T 8: 85,898,172 (GRCm39) L8F probably benign Het
Col17a1 T C 19: 47,637,442 (GRCm39) probably benign Het
Coro6 A T 11: 77,360,293 (GRCm39) N421I probably benign Het
Cps1 T C 1: 67,269,440 (GRCm39) S1480P probably damaging Het
Csrnp3 G T 2: 65,832,826 (GRCm39) A110S probably damaging Het
Cyp2d10 G T 15: 82,287,240 (GRCm39) T461K probably damaging Het
Dmxl2 A G 9: 54,308,769 (GRCm39) V1994A probably benign Het
Dnah11 T A 12: 118,160,379 (GRCm39) N117I probably benign Het
Dnajc3 A G 14: 119,195,307 (GRCm39) Y74C probably damaging Het
Fam13c T A 10: 70,390,403 (GRCm39) F555I possibly damaging Het
Fbn1 T A 2: 125,188,354 (GRCm39) D1495V probably damaging Het
Fbrsl1 T C 5: 110,595,862 (GRCm39) T58A probably benign Het
Gjd3 A G 11: 102,691,706 (GRCm39) I99T possibly damaging Het
Glce T C 9: 61,977,857 (GRCm39) N9S probably damaging Het
Gosr1 T C 11: 76,641,704 (GRCm39) T125A possibly damaging Het
Ifi27l2a T A 12: 103,406,202 (GRCm39) probably null Het
Jph1 C T 1: 17,167,456 (GRCm39) D125N possibly damaging Het
Kbtbd12 A T 6: 88,595,676 (GRCm39) S51R probably damaging Het
Klra9 A T 6: 130,166,659 (GRCm39) probably null Het
Kmo A T 1: 175,484,289 (GRCm39) M340L probably benign Het
Lama1 T C 17: 68,024,181 (GRCm39) I93T possibly damaging Het
Limk2 A T 11: 3,308,104 (GRCm39) probably null Het
Mgat5 C A 1: 127,248,375 (GRCm39) N92K probably benign Het
Mib2 T A 4: 155,739,256 (GRCm39) I908F probably damaging Het
Mical1 T G 10: 41,356,359 (GRCm39) L304R probably damaging Het
Mtbp G T 15: 55,434,690 (GRCm39) probably null Het
Myo3a T C 2: 22,455,004 (GRCm39) Y70H probably damaging Het
Neb T C 2: 52,133,401 (GRCm39) Y3379C probably damaging Het
Neurod2 G T 11: 98,218,029 (GRCm39) N378K probably damaging Het
Oog4 G A 4: 143,166,484 (GRCm39) L107F probably damaging Het
Or2g25 A G 17: 37,970,799 (GRCm39) S142P probably benign Het
Or4k40 T A 2: 111,251,003 (GRCm39) M98L probably benign Het
Or6x1 A G 9: 40,099,161 (GRCm39) Y250C probably damaging Het
Or8k20 T A 2: 86,106,337 (GRCm39) T165S probably damaging Het
Pfdn6 T C 17: 34,158,528 (GRCm39) Y82C probably damaging Het
Pla2g4d C A 2: 120,107,971 (GRCm39) A313S possibly damaging Het
Rai1 A G 11: 60,078,428 (GRCm39) T831A probably benign Het
Rims1 G A 1: 22,367,172 (GRCm39) T1176M probably damaging Het
Rin1 A C 19: 5,105,171 (GRCm39) I744L probably benign Het
Rora T A 9: 69,282,771 (GRCm39) S430T probably benign Het
Rsph10b T A 5: 143,873,967 (GRCm39) S23T probably damaging Het
Ryr1 T C 7: 28,746,928 (GRCm39) N3773S probably benign Het
Scn4a A G 11: 106,230,180 (GRCm39) Y543H probably damaging Het
Scn4a C A 11: 106,236,373 (GRCm39) G296C probably benign Het
Scn7a T C 2: 66,535,447 (GRCm39) T435A probably benign Het
Shank2 G T 7: 143,964,890 (GRCm39) D833Y probably damaging Het
Slc9a2 T C 1: 40,802,770 (GRCm39) S607P possibly damaging Het
Slx4 G A 16: 3,809,458 (GRCm39) R346W probably damaging Het
Spata20 A T 11: 94,371,340 (GRCm39) C675S probably benign Het
Suclg2 A T 6: 95,563,997 (GRCm39) I196N probably damaging Het
Sv2b G A 7: 74,798,807 (GRCm39) H272Y possibly damaging Het
Svep1 T C 4: 58,070,629 (GRCm39) I2386V probably benign Het
Taf13 A T 3: 108,488,445 (GRCm39) E109D possibly damaging Het
Tanc2 A G 11: 105,790,606 (GRCm39) T976A probably benign Het
Tax1bp1 A G 6: 52,706,311 (GRCm39) Y104C probably damaging Het
Tfeb T C 17: 48,099,911 (GRCm39) probably null Het
Tlr9 T C 9: 106,101,248 (GRCm39) Y180H probably damaging Het
Trappc9 G A 15: 72,897,816 (GRCm39) R377W probably damaging Het
Ttc12 T A 9: 49,356,499 (GRCm39) T510S probably benign Het
Ubqln1 T C 13: 58,339,895 (GRCm39) E280G probably damaging Het
Urm1 T C 2: 29,731,437 (GRCm39) W44R probably damaging Het
Usp32 A T 11: 84,933,406 (GRCm39) I34N probably benign Het
Vars1 T C 17: 35,233,728 (GRCm39) L1018P probably damaging Het
Vcan A T 13: 89,869,894 (GRCm39) V206D probably damaging Het
Vim T C 2: 13,583,270 (GRCm39) V224A probably damaging Het
Vmn2r106 G T 17: 20,498,997 (GRCm39) H305N probably benign Het
Vmn2r78 A G 7: 86,604,132 (GRCm39) N770S probably damaging Het
Wdr33 T A 18: 32,029,684 (GRCm39) L961Q unknown Het
Xylt2 A G 11: 94,559,575 (GRCm39) S356P possibly damaging Het
Zbtb14 A G 17: 69,694,575 (GRCm39) N91S probably damaging Het
Zc3h6 T C 2: 128,858,654 (GRCm39) L895S probably damaging Het
Zc3h7b C T 15: 81,661,289 (GRCm39) P376L probably benign Het
Zfp131 T C 13: 120,228,079 (GRCm39) T523A probably benign Het
Other mutations in Ptcd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00767:Ptcd3 APN 6 71,880,432 (GRCm39) missense probably damaging 0.96
IGL00903:Ptcd3 APN 6 71,884,828 (GRCm39) missense possibly damaging 0.93
IGL01545:Ptcd3 APN 6 71,865,561 (GRCm39) missense probably benign 0.01
IGL01924:Ptcd3 APN 6 71,875,411 (GRCm39) missense probably damaging 1.00
IGL02675:Ptcd3 APN 6 71,860,426 (GRCm39) critical splice donor site probably null
R0732:Ptcd3 UTSW 6 71,858,155 (GRCm39) unclassified probably benign
R1374:Ptcd3 UTSW 6 71,885,637 (GRCm39) nonsense probably null
R1393:Ptcd3 UTSW 6 71,866,605 (GRCm39) missense probably benign 0.00
R1498:Ptcd3 UTSW 6 71,870,479 (GRCm39) missense probably damaging 1.00
R1646:Ptcd3 UTSW 6 71,875,379 (GRCm39) missense probably benign 0.26
R2022:Ptcd3 UTSW 6 71,862,537 (GRCm39) missense probably damaging 1.00
R2248:Ptcd3 UTSW 6 71,871,269 (GRCm39) critical splice donor site probably null
R2406:Ptcd3 UTSW 6 71,865,631 (GRCm39) missense probably damaging 1.00
R3418:Ptcd3 UTSW 6 71,860,470 (GRCm39) missense possibly damaging 0.93
R3419:Ptcd3 UTSW 6 71,860,470 (GRCm39) missense possibly damaging 0.93
R4677:Ptcd3 UTSW 6 71,870,498 (GRCm39) missense probably benign 0.17
R4741:Ptcd3 UTSW 6 71,879,933 (GRCm39) missense probably damaging 1.00
R4752:Ptcd3 UTSW 6 71,878,296 (GRCm39) missense probably damaging 0.99
R5441:Ptcd3 UTSW 6 71,858,505 (GRCm39) missense possibly damaging 0.62
R5583:Ptcd3 UTSW 6 71,879,920 (GRCm39) missense probably damaging 1.00
R5681:Ptcd3 UTSW 6 71,884,643 (GRCm39) missense probably damaging 1.00
R6028:Ptcd3 UTSW 6 71,875,392 (GRCm39) missense probably damaging 1.00
R6324:Ptcd3 UTSW 6 71,862,311 (GRCm39) missense probably benign 0.00
R6537:Ptcd3 UTSW 6 71,874,094 (GRCm39) splice site probably null
R6600:Ptcd3 UTSW 6 71,860,530 (GRCm39) missense probably damaging 1.00
R6783:Ptcd3 UTSW 6 71,885,627 (GRCm39) missense probably benign 0.00
R6810:Ptcd3 UTSW 6 71,862,516 (GRCm39) missense probably damaging 0.99
R6860:Ptcd3 UTSW 6 71,874,094 (GRCm39) splice site probably null
R6993:Ptcd3 UTSW 6 71,862,299 (GRCm39) missense probably damaging 1.00
R7578:Ptcd3 UTSW 6 71,885,691 (GRCm39) missense probably benign
R7788:Ptcd3 UTSW 6 71,862,541 (GRCm39) missense probably benign 0.00
R7851:Ptcd3 UTSW 6 71,879,843 (GRCm39) missense probably damaging 1.00
R7888:Ptcd3 UTSW 6 71,860,431 (GRCm39) missense probably damaging 1.00
R7889:Ptcd3 UTSW 6 71,865,592 (GRCm39) missense probably damaging 1.00
R7919:Ptcd3 UTSW 6 71,880,438 (GRCm39) missense probably damaging 1.00
R8162:Ptcd3 UTSW 6 71,884,798 (GRCm39) missense probably benign 0.02
R8351:Ptcd3 UTSW 6 71,885,625 (GRCm39) missense probably benign 0.00
R8451:Ptcd3 UTSW 6 71,885,625 (GRCm39) missense probably benign 0.00
R8701:Ptcd3 UTSW 6 71,862,495 (GRCm39) missense possibly damaging 0.92
R8826:Ptcd3 UTSW 6 71,885,645 (GRCm39) missense probably benign 0.01
R8926:Ptcd3 UTSW 6 71,869,464 (GRCm39) missense probably damaging 1.00
R8969:Ptcd3 UTSW 6 71,880,431 (GRCm39) missense probably benign 0.44
R9031:Ptcd3 UTSW 6 71,880,458 (GRCm39) nonsense probably null
R9046:Ptcd3 UTSW 6 71,870,364 (GRCm39) critical splice donor site probably null
R9384:Ptcd3 UTSW 6 71,874,110 (GRCm39) missense possibly damaging 0.77
R9668:Ptcd3 UTSW 6 71,871,275 (GRCm39) missense possibly damaging 0.93
R9771:Ptcd3 UTSW 6 71,872,903 (GRCm39) nonsense probably null
X0024:Ptcd3 UTSW 6 71,878,258 (GRCm39) missense probably damaging 1.00
X0065:Ptcd3 UTSW 6 71,884,790 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GCGGCACTCACGGAAATGTAAAC -3'
(R):5'- GGCTTGGCAAATTGGCTTGGAC -3'

Sequencing Primer
(F):5'- TCACGGAAATGTAAACTTCACGAG -3'
(R):5'- TCTAGCCAAACAGGACCTTGTG -3'
Posted On 2014-05-14